新疆沙冬青基因组调查测序与基因组大小预测

新疆沙冬青是中国荒漠地区代表性常绿阔叶植物,属于第三纪孑遗植物。其极强的逆境耐受性受到了研究者的广泛关注,但由于缺乏基因组序列,分子生物学研究水平进展缓慢。本研究对新疆沙冬青进行了基因组调查测序,共得到65 Gb大小的双端测序数据。结合基于K-mer分析和流式细胞分析的方法,预测基因组大小、杂合率和GC含量等特征,估计基因组大小为770~787 Mb。测序数据拼接构建得到contigs的N50为684 bp,总读长为0.538 Gb;进一步组装后scaffolds的N50为12.09 kb,总读长为0.602 Gb。对拼接数据进行SSR分子标记预测,共得到151858个SSR,其中二核苷酸重复单元比例最高为56.39%,在二核苷酸重复单元中,AT/TA组成形式占多数。本研究首次报道了荒漠植物新疆沙冬青的基因组特征,为后续基因组学研究提供参考。

Genomic survey sequencing and estimation of genome size of Ammopiptanthus nanus

Ammopiptanthus nanus, one of the tertiary relict plants, is a rare evergreen broad-leaved shrub in desert region of mid-Asia. The plant species can grow in environment with extremely high level of drought and freezing stress, and it can be used as a model for stress tolerance research in tress. However, research in A. nanus at molecular level is hindered by the lack of genome information. In the present study, flow cytometry analysis was performed to predict the genome size of A. nanus. Genomic survey sequencing of A. nanus was then conducted, and a total of 65 Gb sequencing reads was obtained. K-mer analysis using these sequencing reads was conducted to predict the genome size, heterozygosity and GC content of A. nanus. The genome size of A. nanus was estimated to be 770-787 Mb. The total reads length of contigs is 0.538 Gb, with a N50 of 684 bp, and after further assembly, the N50 of scaffords is 12.09 Kb with a total reads length of 0.602 Gb. SSR molecular markers were predicted using the assembled genome sequences and 151858 SSR were obtained. Of all SSR categories, the dinucleotide repeat units is largest, with a percentage of 56.39%, and the AT/TA components is the dominant dinucleotide repeat unit. Our study reported on the genomic characteristics of A nanus for the first time, and provided a large number of genomic sequences for further research in A nanus.